Confidence in evolutionary trees from biological sequence data
- 1 July 1993
- journal article
- letter
- Published by Springer Nature in Nature
- Vol. 364 (6436), 440-442
- https://doi.org/10.1038/364440a0
Abstract
THE reliable construction of evolutionary trees from nucleotide sequences often depends on randomization tests such as the bootstrap1 and FTP (cladistic permutation tail probability) tests2–6. The genomes of bacteria7, viruses8, animals7,9,10 and plants11, however, vary widely in their nucleotide frequencies. Where genomes have independently acquired similar G+C base compositions, signals in the data arise that cause methods of evolutionary tree reconstruction to estimate the wrong tree by grouping together sequences with similar G+C content12–14. Under these conditions randomization tests can lead to both the rejection of the correct evolutionary hypothesis and acceptance of an incorrect hypothesis (such as with the contradictory inferences from the photosynthetic rbcS and rbcL sequences14). We have proposed one approach to testing for the G+C content problem15. Here we present a formalization of this method, a frequency-dependent significance test, which has general application.Keywords
This publication has 18 references indexed in Scilit:
- Significance of the length of the shortest treeJournal of Classification, 1992
- COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURECladistics, 1991
- Chloroplast genes transferred to the nuclear plant genome have adjusted to nuclear base composition and codon usageNucleic Acids Research, 1990
- Nucleotide sequence of the genome of an Australian isolate of turnip yellow mosaic tymovirusVirology, 1989
- Influenza viruses, comets and the science of evolutionary treesJournal of Theoretical Biology, 1989
- A Randomization Test for Phylogenetic Information in Systematic DataSystematic Zoology, 1989
- Models for the origin of influenza virusesNature, 1987
- Compositional constraints and genome evolutionJournal of Molecular Evolution, 1986
- Silent nucleotide substitutions and G+C content of some mitochondrial and bacterial genesJournal of Molecular Evolution, 1986
- CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAPEvolution, 1985